Parameters Input values
Folder name : Example data
Sequence name : Test sequence
Reference genome : BSgenome.Hsapiens.UCSC.hg19
Type of experiment : Cloning-BSP
Group order : group1, group2
Date of analysis : 2023-06-09 17:28

Files content

Data files content

Parameters Data files content
Sequence name : Test sequence
Collections : collection1, collection2
Groups : group1, group2
Clones : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

Data files paths

File paths used for the analysis

D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone01_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone02_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone03_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone04_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone05_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone06_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone07_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone08_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone09_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group1_clone10_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone01_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone02_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone03_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone04_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone05_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone06_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone07_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone08_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone09_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection1_group2_clone10_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone01_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone02_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone03_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone04_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone05_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone06_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone07_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone08_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone09_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group1_clone10_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone01_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone02_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone03_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone04_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone05_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone06_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone07_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone08_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone09_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_cloning/data/Test sequence_collection2_group2_clone10_methdata.csv

Methylation data

Methylation data of clones

For cloning expermients, methylation percentages calculated from sequencing results are converted to 0% or 100% methylation status.

A CpG site is considered unmethylated (0%) when methylation percentage is between 0% and 20%.
A CpG site is considered methylated (100%) when methylation percentage is between 80% and 100%.
A CpG site partially methylated, with methylation percentage between 20% and 80%, is removed and annotated as NA (Not Available).
For one clone, if more than 20% of CpGs are partially methylated, the clone is considered as defective and all of its CpG sites are annotated as NA (Not Available).
chr16:68770595-68770596 chr16:68770613-68770614 chr16:68770646-68770647 chr16:68770665-68770666 chr16:68770670-68770671 chr16:68770717-68770718 Mean SD
collection1 group1 clone 1 0 0 0 100 NA 100 40.00 54.77
collection1 group1 clone 2 0 0 100 0 100 100 50.00 54.77
collection1 group1 clone 3 0 100 0 100 0 0 33.33 51.64
collection1 group1 clone 4 0 100 0 0 0 100 33.33 51.64
collection1 group1 clone 5 0 0 0 100 100 NA 40.00 54.77
collection1 group1 clone 6 NA 0 0 100 0 0 20.00 44.72
collection1 group1 clone 7 0 100 0 0 0 0 16.67 40.82
collection1 group1 clone 8 0 100 0 0 NA 0 20.00 44.72
collection1 group1 clone 9 0 0 0 100 100 100 50.00 54.77
collection1 group1 clone 10 100 0 0 0 0 0 16.67 40.82
collection1 group2 clone 1 100 0 100 100 100 100 83.33 40.82
collection1 group2 clone 2 100 0 100 100 100 100 83.33 40.82
collection1 group2 clone 3 0 100 100 100 100 100 83.33 40.82
collection1 group2 clone 4 100 100 0 100 100 100 83.33 40.82
collection1 group2 clone 5 100 0 0 100 100 100 66.67 51.64
collection1 group2 clone 6 100 0 100 100 100 100 83.33 40.82
collection1 group2 clone 7 100 0 100 100 100 100 83.33 40.82
collection1 group2 clone 8 0 0 100 100 0 100 50.00 54.77
collection1 group2 clone 9 0 100 100 0 100 100 66.67 51.64
collection1 group2 clone 10 0 100 100 0 100 100 66.67 51.64
collection2 group1 clone 1 0 100 100 0 NA 100 60.00 54.77
collection2 group1 clone 2 0 0 100 100 0 0 33.33 51.64
collection2 group1 clone 3 0 100 100 0 100 100 66.67 51.64
collection2 group1 clone 4 NA NA NA NA NA NA NaN NA
collection2 group1 clone 5 100 100 0 0 0 100 50.00 54.77
collection2 group1 clone 6 0 0 0 0 0 0 0.00 0.00
collection2 group1 clone 7 0 0 100 100 0 100 50.00 54.77
collection2 group1 clone 8 0 0 0 100 NA 100 40.00 54.77
collection2 group1 clone 9 0 100 0 0 0 100 33.33 51.64
collection2 group1 clone 10 0 0 100 0 NA 0 20.00 44.72
collection2 group2 clone 1 0 100 100 100 100 100 83.33 40.82
collection2 group2 clone 2 0 100 100 0 100 100 66.67 51.64
collection2 group2 clone 3 100 100 100 100 100 0 83.33 40.82
collection2 group2 clone 4 100 0 100 100 100 0 66.67 51.64
collection2 group2 clone 5 100 100 100 100 100 100 100.00 0.00
collection2 group2 clone 6 100 0 100 100 0 100 66.67 51.64
collection2 group2 clone 7 100 100 0 100 100 100 83.33 40.82
collection2 group2 clone 8 0 100 NA 0 0 100 40.00 54.77
collection2 group2 clone 9 100 100 100 0 100 100 83.33 40.82
collection2 group2 clone 10 0 0 100 0 100 100 50.00 54.77

Methylation data of groups

chr16:68770595-68770596 chr16:68770613-68770614 chr16:68770646-68770647 chr16:68770665-68770666 chr16:68770670-68770671 chr16:68770717-68770718 Mean SD
collection1 group1 11.11 40.00 10.00 50.00 37.50 44.44 32.17 17.28
collection1 group2 60.00 40.00 80.00 80.00 90.00 100.00 75.00 21.68
collection2 group1 11.11 44.44 55.56 33.33 16.67 66.67 37.96 21.78
collection2 group2 60.00 70.00 88.89 60.00 80.00 80.00 73.15 11.81

Plots of clones

collection1 group1

Lollipop plots

Sample order : as-is
Type : proportional

Type : condensed

Sample order : by-meth
Type : proportional

Type : condensed

Sample order : clust
Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-meth

Sample order : clust

collection1 group2

Lollipop plots

Sample order : as-is
Type : proportional

Type : condensed

Sample order : by-meth
Type : proportional

Type : condensed

Sample order : clust
Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-meth

Sample order : clust

collection2 group1

Lollipop plots

Sample order : as-is
Type : proportional

Type : condensed

Sample order : by-meth
Type : proportional

Type : condensed

Sample order : clust
Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-meth

Sample order : clust

collection2 group2

Lollipop plots

Sample order : as-is
Type : proportional

Type : condensed

Sample order : by-meth
Type : proportional

Type : condensed

Sample order : clust
Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-meth

Sample order : clust

Plots of groups

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Sample order : by-group

Type : proportional

Type : condensed

Sample order : by-meth

Type : proportional

Type : condensed

Sample order : clust

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-group

Sample order : by-meth

Sample order : clust

Statistics

Descriptive statistics of groups

Methylation means of all CpG positions

Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
collection1 group1 10 32.00 13.07 4.13 9.35
collection1 group2 10 75.00 11.78 3.73 8.43
collection2 group1 9 39.26 20.60 6.87 15.84
collection2 group2 10 72.33 17.92 5.67 12.82

Methylation by CpG positions

CpG number CpG coordinate Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
1 chr16:68770595-68770596 collection1 group1 9 11.11 33.33 11.11 25.62
1 chr16:68770595-68770596 collection1 group2 10 60.00 51.64 16.33 36.94
1 chr16:68770595-68770596 collection2 group1 9 11.11 33.33 11.11 25.62
1 chr16:68770595-68770596 collection2 group2 10 60.00 51.64 16.33 36.94
2 chr16:68770613-68770614 collection1 group1 10 40.00 51.64 16.33 36.94
2 chr16:68770613-68770614 collection1 group2 10 40.00 51.64 16.33 36.94
2 chr16:68770613-68770614 collection2 group1 9 44.44 52.70 17.57 40.51
2 chr16:68770613-68770614 collection2 group2 10 70.00 48.30 15.28 34.56
3 chr16:68770646-68770647 collection1 group1 10 10.00 31.62 10.00 22.62
3 chr16:68770646-68770647 collection1 group2 10 80.00 42.16 13.33 30.16
3 chr16:68770646-68770647 collection2 group1 9 55.56 52.70 17.57 40.51
3 chr16:68770646-68770647 collection2 group2 9 88.89 33.33 11.11 25.62
4 chr16:68770665-68770666 collection1 group1 10 50.00 52.70 16.67 37.70
4 chr16:68770665-68770666 collection1 group2 10 80.00 42.16 13.33 30.16
4 chr16:68770665-68770666 collection2 group1 9 33.33 50.00 16.67 38.43
4 chr16:68770665-68770666 collection2 group2 10 60.00 51.64 16.33 36.94
5 chr16:68770670-68770671 collection1 group1 8 37.50 51.75 18.30 43.27
5 chr16:68770670-68770671 collection1 group2 10 90.00 31.62 10.00 22.62
5 chr16:68770670-68770671 collection2 group1 6 16.67 40.82 16.67 42.84
5 chr16:68770670-68770671 collection2 group2 10 80.00 42.16 13.33 30.16
6 chr16:68770717-68770718 collection1 group1 9 44.44 52.70 17.57 40.51
6 chr16:68770717-68770718 collection1 group2 10 100.00 0.00 0.00 0.00
6 chr16:68770717-68770718 collection2 group1 9 66.67 50.00 16.67 38.43
6 chr16:68770717-68770718 collection2 group2 10 80.00 42.16 13.33 30.16

Student’s T test

For means of CpG positions

Student’s T test (two-samples, unpaired).

Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
collection1 group1 group2 10 10 4.30e-07 ****
collection2 group1 group2 9 10 1.88e-03 **

For each CpG position

Student’s T test (two-samples, unpaired).

CpG number CpG coordinate Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
1 chr16:68770595-68770596 collection1 group1 group2 9 10 0.025300 *
2 chr16:68770613-68770614 collection1 group1 group2 10 10 1.000000 ns
3 chr16:68770646-68770647 collection1 group1 group2 10 10 0.000624 ***
4 chr16:68770665-68770666 collection1 group1 group2 10 10 0.178000 ns
5 chr16:68770670-68770671 collection1 group1 group2 8 10 0.028500 *
6 chr16:68770717-68770718 collection1 group1 group2 9 10 0.013300 *
1 chr16:68770595-68770596 collection2 group1 group2 9 10 0.025300 *
2 chr16:68770613-68770614 collection2 group1 group2 9 10 0.288000 ns
3 chr16:68770646-68770647 collection2 group1 group2 9 9 0.132000 ns
4 chr16:68770665-68770666 collection2 group1 group2 9 10 0.269000 ns
5 chr16:68770670-68770671 collection2 group1 group2 6 10 0.012900 *
6 chr16:68770717-68770718 collection2 group1 group2 9 10 0.541000 ns

Boxplots

For means of CpG positions

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

collection1
p-values significance levels

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p-values

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without p-values

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collection2
p-values significance levels

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p-values

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without p-values

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For each CpG position

Individual clone methylation is represented as a round shape and the methylation mean of clones as a diamond shape.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

collection1
p-values significance levels

Open boxplot image in a new tab.

p-values

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without p-values

Open boxplot image in a new tab.

collection2
p-values significance levels

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p-values

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without p-values

Open boxplot image in a new tab.

Methylation profile plots

Each points represent the methylation mean of clones or replicates for a given CpG site.
The p-values and p-value significance levels are determined by Kruskal-Wallis tests.

collection1

Type : proportional
p-values significance levels

p-values

without p-values

Type : condensed
p-values significance levels

p-values

without p-values

collection2

Type : proportional
p-values significance levels

p-values

without p-values

Type : condensed
p-values significance levels

p-values

without p-values

Output data

Directories

Files

lollipop_plots

Test sequence_lollipop_clones_as-is_condensed_collection1_group1.png

Test sequence_lollipop_clones_as-is_condensed_collection1_group2.png

Test sequence_lollipop_clones_as-is_condensed_collection2_group1.png

Test sequence_lollipop_clones_as-is_condensed_collection2_group2.png

Test sequence_lollipop_clones_as-is_proportional_collection1_group1.png

Test sequence_lollipop_clones_as-is_proportional_collection1_group2.png

Test sequence_lollipop_clones_as-is_proportional_collection2_group1.png

Test sequence_lollipop_clones_as-is_proportional_collection2_group2.png

Test sequence_lollipop_clones_by-meth_condensed_collection1_group1.png

Test sequence_lollipop_clones_by-meth_condensed_collection1_group2.png

Test sequence_lollipop_clones_by-meth_condensed_collection2_group1.png

Test sequence_lollipop_clones_by-meth_condensed_collection2_group2.png

Test sequence_lollipop_clones_by-meth_proportional_collection1_group1.png

Test sequence_lollipop_clones_by-meth_proportional_collection1_group2.png

Test sequence_lollipop_clones_by-meth_proportional_collection2_group1.png

Test sequence_lollipop_clones_by-meth_proportional_collection2_group2.png

Test sequence_lollipop_clones_clust_condensed_collection1_group1.png

Test sequence_lollipop_clones_clust_condensed_collection1_group2.png

Test sequence_lollipop_clones_clust_condensed_collection2_group1.png

Test sequence_lollipop_clones_clust_condensed_collection2_group2.png

Test sequence_lollipop_clones_clust_proportional_collection1_group1.png

Test sequence_lollipop_clones_clust_proportional_collection1_group2.png

Test sequence_lollipop_clones_clust_proportional_collection2_group1.png

Test sequence_lollipop_clones_clust_proportional_collection2_group2.png

Test sequence_lollipop_groups_as-is_condensed.png

Test sequence_lollipop_groups_as-is_proportional.png

Test sequence_lollipop_groups_by-group_condensed.png

Test sequence_lollipop_groups_by-group_proportional.png

Test sequence_lollipop_groups_by-meth_condensed.png

Test sequence_lollipop_groups_by-meth_proportional.png

Test sequence_lollipop_groups_clust_condensed.png

Test sequence_lollipop_groups_clust_proportional.png